MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3owi 3OWI (2.85Å) -- RNA : Crystal structure of the glycine riboswitch bound to glycine List of all 15 Mg2+ binding sites in the PDB structure 3owi in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 1 of 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3owi B112 Nb G:B62(N7) B141, B142, B143, B144, B145 G:B62, U:B61, C:B39 3owi A115 Nb G:A50(N7) A172, A173, A174, A175, A176 G:A49, A:B52 G:A49 3owi A116 Oph·Pout A:A78(OP2) A177, A178, A179, A180, A181 A:A77 A:A78, G:A79, G:A80 3owi A118 Oph·Pout A:A21(OP2) A182, A183, A184, A185, A186 A:A51 U:A19 A:A21, A:A22, U:A23, A:B53 3owi B117 Oph·Pout U:B23(OP1) B153, B154, B155, B156, B157 G:B25 G:B26, G:B25 3owi A111 Oph·3Pout U:A20(OP2) A167, A168, A169, A170, A171 A:A21, C:A15, G:B25 C:B24 3owi B113 cis-2Oph A:B34(OP1), G:B35(OP2) B146, B147, B148, B149 A:B81 G:B35, G:B36 3owi A105 cis-2Oph C:A70(OP2), A:A71(OP2) A146, A147, A148, A149 U:A69 G:A72, A:A71 3owi A101 cis-2Oph A:A34(OP1), G:A35(OP2) A132, A133, A134, A135 A:A81 G:A35, G:A36 3owi A103 trans-2Oph A:A22(OP1), A:A75(OP2) A139, A140, A141, A142 C:A74 A:A75 3owi A102 cis-2Oph·Or A:A33(OP2), C:A66(OP2) G:A32(O2') A136, A137, A138 U:A69 3owi B114 cis-2Oph·Or A:B33(OP2), C:B66(OP2) G:B32(O2') B150, B151, B152 U:B69, U:B67 3owi A104 mer-3Oph C:A74(OP1), A:A75(OP1), A:A76(OP2) A143, A144, A145 A:A76, A:A77 3owi B108 4Pout B135, B136, B137, B138, B139, B140 G:A10, U:B67, G:B32, C:B68 3owi A107 4Pout A150, A151, A152, A153, A154, B134 G:A32, U:A67, C:A68, G:B10

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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